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Short- and long-rea...
Short- and long-read metabarcoding of the eukaryotic rRNA operon : Evaluation of primers and comparison to shotgun metagenomics sequencing
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- Latz, Meike (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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- Grujcic, Vesna, 1988- (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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- Brugel, Sonia (författare)
- Umeå universitet,Institutionen för ekologi, miljö och geovetenskap,EcoChange; UMFpub
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- Lycken, J. (författare)
- Oceanographic Research, Swedish Meteorological and Hydrological Institute, Gothenburg, Sweden
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- John, U. (författare)
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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- Karlson, B. (författare)
- Oceanographic Research, Swedish Meteorological and Hydrological Institute, Gothenburg, Sweden
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- Andersson, Agneta (författare)
- Umeå universitet,Institutionen för ekologi, miljö och geovetenskap,EcoChange; UMFpub
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- Andersson, Anders F. (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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(creator_code:org_t)
- 2022-05-06
- 2022
- Engelska.
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 22:6, s. 2304-2318
- Relaterad länk:
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https://doi.org/10.1...
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https://umu.diva-por... (primary) (Raw object)
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.
Ämnesord
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Nyckelord
- marine plankton
- metabarcoding
- microbial eukaryotes
- PacBio long-read sequencing
- primer design
- rRNA operon
- primer DNA
- RNA 16S
- RNA 18S
- eukaryote
- genetics
- high throughput sequencing
- metagenomics
- operon
- phylogeny
- procedures
- DNA Primers
- Eukaryota
- High-Throughput Nucleotide Sequencing
- RNA
- Ribosomal
- 16S
- RNA
- Ribosomal
- 18S
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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